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comparison tetyper.xml @ 2:edcf603bedfd draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit a5b87b732eb5016450c39c07be4f5de95ff81fc7"
author iuc
date Tue, 16 Nov 2021 19:57:38 +0000
parents 36093854bfc7
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1:36093854bfc7 2:edcf603bedfd
6 <requirements> 6 <requirements>
7 <requirement type="package" version="@TOOL_VERSION@">tetyper</requirement> 7 <requirement type="package" version="@TOOL_VERSION@">tetyper</requirement>
8 </requirements> 8 </requirements>
9 <command detect_errors="exit_code"> 9 <command detect_errors="exit_code">
10 <![CDATA[ 10 <![CDATA[
11 ## avoid creating indices in the inputdir
12 ln -s '$reference' reference.fa &&
11 TETyper.py 13 TETyper.py
12 --threads \${GALAXY_SLOTS:-1} 14 --threads \${GALAXY_SLOTS:-1}
13 #if $collection_paired.selector == "paired" 15 #if $collection_paired.selector == "paired"
14 --fq1 '${collection_paired.forward_input}' --fq2 '${collection_paired.reverse_input}' 16 --fq1 '${collection_paired.forward_input}' --fq2 '${collection_paired.reverse_input}'
15 #elif $collection_paired.selector == "collection": 17 #elif $collection_paired.selector == "collection":
16 --fq1 '${collection_paired.input_pair.forward}' --fq2 '${collection_paired.input_pair.reverse}' 18 --fq1 '${collection_paired.input_pair.forward}' --fq2 '${collection_paired.input_pair.reverse}'
17 #end if 19 #end if
18 --ref '${reference}' 20 --ref 'reference.fa'
19 --flank_len '${flank_length}' 21 --flank_len '${flank_length}'
20 --min_reads '${min_reads}' 22 --min_reads '${min_reads}'
21 --min_each_strand '${min_each_strand}' 23 --min_each_strand '${min_each_strand}'
22 --min_mapped_len '${min_mapped_len}' 24 --min_mapped_len '${min_mapped_len}'
23 --min_qual '${min_qual}' 25 --min_qual '${min_qual}'